Table 1.

Comparison of average CPU time for various RNA structural alignment tools

Data set	ARTS	PARTS	SARA	LaJolla	iPARTS
tRNA	38.7 s	2.8 s	5 s	1.1 s	1 s
Ribozyme P4-P6 domain	52.4 s	5.5 s	12.9 s	5.2 s	2.8 s
Domain V of 23S rRNA	79.8 s	22.1 s	N/A	119 s	17.7 s
16S rRNA	3.4 min	2.3 min	N/A	5 h 9 min	2.9 min

Notice that LaJolla was performed using its stand-alone program (because it currently provides no web server for public access), while other tools were performed via their web servers. All these tools were tested using their default parameters. At the time of our testing, the SARA web server cannot deal with domain V of 23S rRNA as well as 16S rRNA.